Lane Coutell, a college student, stands on a train platform waiting for his girlfriend to arrive. He reads a letter of hers for about the fifth time in which she, rather humbly, discusses her love for Sappho (an Ancient Greek poet) and for him, Lane. When Franny arrives however, Lane pretends he barely remembers the letter and tries to hide how excited he is to see her.
As the two of them head to a fancy French restaurant to have lunch together, it quickly becomes clear these two college coeds have some relationship problems. Franny claims to have missed Lane, but quickly realizes she doesn't mean her words at all. Lane comes off as pretentious, and Franny is torn between her annoyance at Lane and her anger at herself for being critical.
It seems that Franny has been going through this judgmental, angry phase for some time now. She resents the whole college system because she thinks her professors are egotistical. We find out that she recently quit her theater activities (she was an actress at school) because she was afraid of becoming egotistical herself.
Meanwhile, Franny has been carrying a little pea-green, cloth-bound book in her purse. Eventually, she divulges the nature of the book and its importance to Lane, who isn't really listening at all. The book is The Way of the Pilgrim, a 19th century religious story about a devout man who travels all over the world reciting the Jesus Prayer. He's taught that if he says it constantly, eventually it will move down from his lips and become part of his soul. Lane does ask if she really believes in this stuff, but Franny dodges the question. Throughout their entire meal, Franny has looked sweaty and pale – and she hasn't touched her meal at all.
Confirming our suspicion that something is wrong, Franny collapses on the way to the bar. Lane and the manager take care of her, and it's clear that she's OK (we suspect that she hasn't eaten in some time and that has something to do with her collapse). As Lane goes to get a cab for them, the story ends with Franny, alone, staring up at the ceiling, her lips forming soundless words, which we figure to be the Jesus Prayer.
"Zooey" begins with an "author's introduction," which is fictional and part of the story. The "author" warns us that his tale will be excruciatingly personal, and that its main characters argued with him about how they should be portrayed. After several pages of this cryptic stuff, we finally figure out that the narrator is Buddy Glass, Franny's older brother. However, once the introduction ends, he tells the story in the third-person instead of the first.
Before we can continue the story, we need some background on the Glass family. Bessie and Les are the parents, and are former vaudeville dancers. They have seven kids who are, by now in 1955, all grown up: Seymour Glass, who killed himself seven years ago (for more, check out "A Perfect Day for Bananafish"); Buddy Glass, our hidden narrator and a writer and teacher at a girls' college; Boo Boo, a wife and mother; Walt, who died in a freak explosion ten years ago; Waker, his twin, who is a Catholic Priest; Zooey, the focus of this story and an actor; and the youngest, Franny, whom we've already met.
The Glass family is peculiar. The children are all incredibly intelligent (to say that they are geniuses would not be inaccurate) and well-read. As children, they were all on a radio show called "It's a Wise Child," where they became child celebrities by answering questions and entertaining audiences with their precociousness. The four children this story deals with most directly – Zooey, Franny, Buddy, and Seymour – also share a sort of social deficiency. They're so smart and well-read that they have trouble fitting in with most people. As we saw of Franny earlier, they can also be judgmental and cynical.
Let's get to the story. The narrator opens his tale with Zooey, who is 25 and incredibly good-looking, sitting in a bathtub smoking and reading a four-year-old letter from his brother Buddy. The letter was written to Zooey when he was finishing college and about to dive headfirst into his acting career. It seems the Glass boys' mother, Bessie, begged Buddy to write Zooey a letter advising him to get a Ph.D. first. The letter, however, which is several pages long and reprinted in full in the text, sidetracks quite a bit. Buddy ends up talking about their oldest brother, Seymour, who killed himself, and the effect that such a suicide has had on the family.
As the letter continues, we realize that Franny is not the only Glass sibling preoccupied with religion. Buddy and Seymour, the oldest two boys, have studied religion and philosophy extensively, and in fact educated Franny and Zooey in such matters when the younger siblings were small.
Zooey's bath is interrupted by the entrance of his mother, Bessie, into the bathroom. It seems that Franny has just come home, having collapsed in a restaurant with Lane. She's holed up on the living room couch sobbing and refusing to eat and claiming that she won't to go back to college. Bessie is distraught and wants Zooey to go in there and talk to his sister.
Eventually, Zooey reveals to his mother the truth about his sister's crisis. He explains about the book Franny has been reading, The Way of the Pilgrim, and its sequel, The Pilgrim Continues His Way. Zooey says that Franny actually got the book from Seymour and Buddy's bookshelves. This launches him into an angry rant against his older brothers – he thinks they are responsible for making life hard for him and Franny. By teaching them so much religion and philosophy when they were so young, Buddy and Seymour messed up the two youngest Glass siblings. Zooey claims he and Franny are now incapable of living normal lives, because they're so preoccupied with spiritual manners.
Eventually, Zooey talks with his sister. Franny reveals a lot of the same dissatisfaction that she earlier expressed to Lane. Zooey ends up critiquing Franny's "breakdown" and even criticizing her. This doesn't go over too well, and she ends up sobbing into the couch. Zooey leaves her alone and goes into the bedroom that Buddy and Seymour used to share. He looks over his brothers' things for a while and then turns to the phone on the desk. Buddy and Seymour had a private phone line, separate from the rest of the house. Zooey picks up the phone and dials the Glass house number.
Zooey pretends to be his older brother Buddy while he talks to Franny on the phone. By the time she figures out the trick, she's just too tired to be mad at Zooey anymore. The two reconcile, Franny finally listens to what Zooey has to say, and she effectively resolves her spiritual and personal crisis.